SEO & Web Marketing Forum

I have noticed last week that my index.php file in root directory is filled up with more then 1000 links. I don't know where it came from. I tried to remove them 2 days back and today i seen my website was closed because of error in index.php. file name was changed as indexold.php. then i again removed all links from index.php and renamed, but i am not sure how long this will work. This is very frustrating situation for me. My RSS feed was not working for month because of change and link stuff in index.php. I also checked my web page source there is code e <!-- e06ee59c42cd12c5c5d4a4c3228998de --> at last line of page, i think that code is also added by hacker. I like to know if anybody else had same problem like this?

I also got this code in my WordPress blog.
<!--08a19398787948d9b2a13f6f1b8f50af-->